Glycoside Hydrolases

Prof. Arun Goyal, M.Sc., M.Tech., Ph.D., is currently a Professor in the Department of Biosciences and Bioengineering, at the Indian Institute of Technology Guwahati, in Assam, India. Prof. Goyal has over 18 years of teaching and 30 years of research experience. His research mainly focuses on structure and functional analysis of plant cell wall degrading enzymes and their applications. Prof. Goyal obtained his M.Sc. and M.Tech. degrees from the Indian Institute of Technology Delhi and Ph.D. from the Indian Institute of Technology Kanpur, India. Prof. Goyal has handled many national and international collaborative research projects, sponsored by various funding agencies of the Government of India such as DBT, DST and CSIR. So far 30 students have obtained Ph.D. under his supervision and 12 students are continuing their Ph.D. Prof. Goyal has published more than 265 research papers in various National and International reputed journals and over 30 book chapters. Dr. Kedar Sharma, M.Sc., Ph.D. currently working as Visiting Fellow at National Institute of Environmental Health Sciences, North Carolina, USA. He worked as Postdoctoral Research Associate, at Department of Biological Engineering, at Indian Institute of Technology Gandhinagar, Gujarat, India. Dr. Sharma has over 7 years of research experience. He completed his Bachelors of Science in Biotechnology from University of Rajasthan, Jaipur and his Masters in Biotechnology from Guru Ghasidas Vishwavidyalaya (Central University) Bilaspur, Chhattisgarh, India. He completed Ph.D. from Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati. His Ph.D. work as focused on structural and functional characterization of xylanolytic enzymes and other glycoside hydrolases and their application in production of xylooligosaccharides. Currently, he is working on elucidating the structure and fusion mechanism of viral entry into the host cell. He received a IUCr Young Scientist award from International Union for Crystallography, and several best poster and oral presentation awards from different organizations. Dr. Sharma has published 33 research papers in various international reputed journals and 5 book chapters.

• Contributors About the EditorsPrefaceCHAPTER 1 Carbohydrates and Carbohydrate-Active enZymes (CAZyme): An overviewParmeshwar Vitthal Gavande, Arun Goyal, and Carlos M.G.A. Fontes1.1 Introduction1.1.1 Various carbohydrate polymers present in nature1.1.2 Natural source of polysaccharides1.1.3 Requirement for deconstruction of carbohydrates1.1.4 Carbohydrate-active enzymes1.1.5 Carbohydrate-active enzyme database (CAZy)1.1.6 Multienzyme complexes of CAZyme: The cellulosome1.1.7 Commercially available CAZyme libraries1.2 ConclusionReferencesCHAPTER 2 Glycoside hydrolases: Mechanisms, specificities, and engineeringAntoni Planas2.1 Structures, functions, and classifications2.2 Glycosidase mechanisms for hydrolysis of glycans and glycoconjugates2.2.1 General mechanisms: Inverting vs. retaining2.2.2 Retaining glycosidases with enzyme nucleophile: Ring distortion and covalent intermediate2.2.3 Retaining glycosidases by substrate-assisted catalysis: Oxazoline/oxazolonium intermediate2.2.4 Retaining glycosidases by neighboring-group participation through a 1,2-epoxide intermediate2.2.5 Retaining glycosidases by an unusual NAD+-dependent mechanism2.2.6 Inverting glycosidases2.3 Protein engineering of glycosidases for improved and novel properties2.3.1 Thermostability2.3.2 Substrate specificity2.4 Glycosidases acting in reverse for glycosynthesis: Transglycosidases and glycosynthases 2.4.1 Transglycosidases2.4.2 Glycosynthases2.5 Concluding remarksReferencesCHAPTER 3 Endo-β-1,4-glucanaseParmeshwar Vitthal Gavande and Arun Goyal3.1 Introduction3.1.1 Cellulase3.1.2 Cellulase evolution and conservation in nature3.1.3 Endo-β-1,4-glucanase3.1.4 Exoglucanase3.1.5 β-glucosidase3.1.6 Cellulosome3.2 Endoglucanases belong to various GH families3.2.1 GH5 family3.2.2 GH6 family3.2.3 GH7 family3.2.4 GH8 family3.2.5 GH9 family3.2.6 GH12 family3.2.7 GH44 family3.2.8 GH45 family3.2.9 GH48 family3.3 Synergism of endo-β-1,4-glucanase with exoglucanase and β-glucosidase3.4 Endo-β-1,4-glucanase-producing microorganisms3.4.1 Biochemical properties, kinetics, and catalytic efficiency of endoglucanases3.5 Structure of endo-β-1,4-glucanases3.5.1 Mechanism of cellulose hydrolysis in endoglucanases3.6 Multifunctionality of endoglucanases3.6.1 Broad substrate specificity of various endoglucanases3.6.2 Significance of multifunctional endoglucanases3.7 Processivity of endoglucanases3.8 Applications of endoglucanases3.9 ConclusionAuthors’ contributionReferencesCHAPTER 4 CellobiohydrolasesTulika Sinha, Kanika Sharma, and Syed Shams Yazdani4.1 Introduction4.2 Structure and mode of action of cellobiohydrolases4.2.1 The catalytic domain (CD)4.2.2 The carbohydrate-binding module (CBM)4.2.3 The linker4.2.4 The dissociation mechanism of processive CBH14.3 Biochemical and biophysical properties of cellobiohydrolases4.3.1 pH and temperature4.3.2 Metal ions4.3.3 Surfactants4.4 Protein engineering and strain improvement for higher enzyme activity and productivity4.4.1 Enhanced activity4.4.2 Enhanced thermostability4.4.3 Enhanced performance in nonconventional media4.4.4 Engineering cellulase for pH stability4.5 Industrial applications of CBH4.5.1 Bioconversion4.5.2 Pulp and paper industry4.5.3 Food processing industry4.5.4 Textile industry4.5.5 Agriculture4.5.6 Animal feed4.5.7 Detergent industry4.6 Conclusion and future perspectiveReferencesCHAPTER 5 β-Glucosidase: Structure, function and industrial applicationsSauratej Sengupta, Maithili Datta, and Supratim Datta5.1 Introduction5.2 Classification 5.3 Structure5.4 Reaction mechanism5.4.1 Substrate recognition and specificity5.4.2 Glycone and aglycone specificity5.5 Function and distribution5.6 Characteristics5.6.1 Biophysical characteristics5.6.2 Biochemical characteristics5.6.3 Product inhibition and enhancement of activity in the presence of glucose 5.6.4 Substrate inhibition5.7 Industrial applications5.7.1 Biofuels5.7.2 Food industry5.7.3 Pharmaceutical industriesAcknowledgmentsReferencesCHAPTER 6 Endo-β-1,3-glucanaseParmeshwar Vitthal Gavande and Arun Goyal6.1 Introduction6.2 The role of endo-β-1,3-glucanase in nature6.2.1 β-1,3-Glucan6.2.2 Exo-β-1,3-glucanase6.2.3 Endo-β-1,3-glucanase6.2.4 Classification of endo-β-1,3-glucanases6.3 Sources of endo-β-1,3-glucanase6.4 Endo-β-1,3-glucanases of different families, their structure, and mechanism 6.4.1 The family GH5 6.4.2 The family GH16 6.4.3 The family GH17 6.4.4 The family GH55 6.4.5 The family GH64 6.4.6 The family GH816.4.7 The family GH128, GH152, GH157, GH1586.5 Applications of endo-β-1,3-glucanases6.6 ConclusionReferencesFurther readingCHAPTER 7 Diversity of microbial endo-β-1,4-xylanasesPeter Biely, Katarı´na Sˇuchova´, and Vladimı´r Puchart7.1 Introduction7.2 Chemical structure of plant xylans7.3 Enzymes of xylan hydrolysis7.4 Endoxylanases—Xylan depolymerizing enzymes7.4.1 Molecular architecture of xylanases7.4.2 Classification into glycoside hydrolase families7.4.3 Mode of action and structure-function relationship7.5 Synergism of endoxylanases with debranching xylanolytic enzymes 7.6 Application of xylanases7.7 Conclusions and future prospectsReferencesCHAPTER 8 β-D-Xylosidases: Structure-based substrate specificities and their applicationsSatoshi Kaneko and Zui Fujimoto8.1 Introduction8.2 Structures of β-xylosidases8.2.1 GH38.2.2 GH398.2.3 GH438.2.4 GH528.2.5 GH1208.2.6 Other families8.3 Substrate specificities of the β-xylosidases8.3.1 GH1 8.3.2 GH2 8.3.3 GH3 8.3.4 GH58.3.5 GH108.3.6 GH11 8.3.7 GH30 8.3.8 GH398.3.9 GH438.3.10 GH518.3.11 GH528.3.12 GH548.3.13 GH116 8.3.14 GH1208.4 Applications of β-xylosidasesReferencesCHAPTER 9 ArabinofuranosidasesPriyanka Pisalwar, Austin Fernandes, Devashish Tribhuvan, Saurav Gite, and Shadab Ahmed9.1 Introduction9.2 Classification9.2.1 Classification on the basis of substrate specificity and mechanism of action 9.2.2 Classification on the basis of amino acid sequencing and structural similarity9.3 Structural and functional characteristics of arabinofuranosidases9.3.1 Effect of metal ions9.3.2 Carbohydrate-binding modules (CBM) associated with arabinofuranosidases 9.4 Substrate specificity and biochemical properties of arabinofuranosidases9.4.1 Substrate specificity9.4.2 Physical and chemical properties9.5 Industrial applications of arabinofuranosidase9.5.1 Biofuel and biochemical industry9.5.2 Food and animal feed industry 9.5.3 Beverage industry9.5.4 Paper and pulp industry9.5.5 Probiotic and pharmaceutical industry9.6 Future trends and scope of arabinofuranosidases9.6.1 Protein engineering9.6.2 Development of new modular enzymes with enhanced substrate degradation potential9.7 ConclusionsReferencesCHAPTER 10 Glycoside hydrolase family 16—Xyloglucan:xyloglucosyl transferases and their roles in plant cell wall structure and mechanics Barbora Stratilova´, Stanislav Kozmon, Eva Stratilova´, and Maria Hrmova10.1 Plant cell walls are protective multicomposite hydrogels10.1.1 Plant cell wall composition and function10.1.2 Plant cell wall structure and organization 10.2 Plant xyloglucan:xyloglucosyl transferases10.2.1 Nomenclature and classification10.2.2 Catalytic mechanism10.2.3 Structural properties10.2.4 Enzyme activity methods10.2.5 Reactions with xyloglucan-derived and other substrates10.2.6 Genetics approaches to the XTH gene function10.3 The function of XTH enzymes in plant cell walls10.3.1 Plant cell wall dynamics10.3.2 Roles of XTH enzymes in cell wall restructuring10.4 Conclusions and future directionsAuthor contributionsFundingConflict of interestReferencesCHAPTER 11 Endo-arabinase: Source and applicationDixita Chettri and Anil Kumar Verma11.1 Introduction11.2 Hemicellulose structure and hydrolysis of arabinans11.3 Source and biochemical characteristics11.4 Structure and mechanism of action11.5 Application of arabinase11.6 Safety assessment11.7 Conclusion and future prospectsAcknowledgmentConflict of interestReferencesCHAPTER 12 Overview of structure-function relationships of glucuronidasesSamar Ballabha Mohapatra and Narayanan Manoj12.1 Introduction12.2 Xylanolytic α-glucuronidases12.2.1 GH67 α-glucuronidases12.2.2 GH115 α-glucuronidases12.3 Non-xylanolytic GH4 α-glucuronidase12.3.1 Active site architecture and the substrate specificity of GH4 TmAgu4B 12.3.2 Mechanism of hydrolysis by GH4 AguA12.4 β-Glucuronidases12.4.1 GH1 β-glucuronidase12.4.2 GH2 β-glucuronidases12.4.3 GH30 β-glucuronidase12.4.4 GH79 β-glucuronidases12.4.5 GH154 β-glucuronidase12.4.6 GH169 β-glucuronidase12.5 Perspectives on the development of applications of glucuronidases12.5.1 Xylanolytic α-glucuronidases12.5.2 Inhibitors of β-glucuronidasesCreditReferencesCHAPTER 13 Mannanases and other mannan-degrading enzymesCaio Cesar de Mello Capetti, Andrei Nicoli Gebieluca Dabul, Vanessa de Oliveira Arnoldi Pellegrini, and Igor Polikarpov13.1 Mannan structure13.2 Enzymes involved in the mannan degradation13.2.1 β-mannanases13.2.2 Other enzymes important for mannan degradation13.3 Production of β-mannanases13.4 Industrial applications of β-mannanases13.4.1 Oil drilling13.4.2 Biofuel production13.4.3 Production of manno-oligosaccharides13.4.4 Paper and pulp production13.4.5 Textile industry13.4.6 Detergents13.4.7 Pharmaceutical and food industry13.5 Concluding remarksReferencesCHAPTER 14 Structure, function, and protein engineering of GH53 β-1,4-galactanasesSebastian J. Muderspach, Kenneth Jensen, Kristian B.R.M. Krogh, and Leila Lo Leggio14.1 Introduction, classification, and structure overview of β-1,4-galactanases14.2 Biological functions and diversity14.2.1 Galactans in the plant cell walls14.2.2 Degradation of plant cell wall galactans in plant pathogens via GH53 enzymes 14.2.3 Characterized GH53 galactanases from human gut microbiome14.2.4 Plant cell wall remodeling for mobilization of energy resources or fruit ripening14.2.5 GH53 galactanases from extremophiles14.3 Related enzyme activities14.3.1 Other microbial endo-galactanases14.3.2 β-galactosidases and exo-β-1,4-galactanases14.3.3 α-L-arabinofuranosidase and endo-1,5-α-L-arabinanase14.4 GH53-associated modules and domains14.4.1 Association of GH53 with carbohydrate-binding modules14.4.2 Association of GH53 with other domains14.5 Biotechnological applications14.5.1 GH53 galactanases in enzymatic degradation of biomass14.5.2 Prebiotic galactooligosaccharide production14.5.3 Other industrial uses14.6 Structure-function studies14.6.1 Conformation of substrate in a computationally derived BlGal-galactononaose complex14.6.2 Substrate-binding sites in GH53 galactanase crystal structures and their implication on product profile14.6.3 Structural features inducing thermostability in GH53 galactanases14.6.4 Prediction of structural features from sequence alignments and AlphaFold models 14.7 Protein engineering14.7.1 Modulating thermostability and pH optimum14.7.2 Changing the product profile14.8 Conclusions and future directionsReferencesCHAPTER 15 Structural and functional insights and applications of β galactosidaseAzra Shafi and Qayyum Husain15.1 β Galactosidase15.2 Glycoside hydrolase families15.3 Sources of β-galactosidases15.3.1 Bacterial β-Gals15.3.2 β-Gals from filamentous fungi15.3.3 β-Gals from yeasts15.3.4 β-Gals from plants15.3.5 β-Gals from animals15.3.6 Recombinant β-Gals15.4 Lactose intolerance15.5 Structural characterization of β-Gal15.5.1 The active site15.5.2 Metal binding sites15.6 Functional characterization of β-Gal15.6.1 Mode of action and reaction mechanism15.6.2 Hydrolysis and transgalactosylation activities of β-Gal15.7 Applications of β-Gal15.7.1 Lactose-hydrolyzed milks15.7.2 β-Gal supplements15.7.3 Treatment of industry effluents15.7.4 Synthesis of GOS15.7.5 Reactors and biosensors15.8 ConclusionReferencesCHAPTER 16 α-L-Rhamnosidases: Structures, substrate specificities, and their applicationsSatoshi Kaneko and Zui Fujimoto16.1 Introduction16.2 Structure of α-L-rhamnosidases16.2.1 GH7816.2.2 GH106 16.3 Substrate specificities of α-L-rhamnosidases16.3.1 GH78 16.3.2 GH106 16.3.3 Unknown family16.4 Applications of α-L-rhamnosidasesReferencesCHAPTER 17 Diversity and biotechnological applications of microbial glucoamylasesSanjeev Kumar, Priyakshi Nath, Arindam Bhattacharyya, Suman Mazumdar, Rudrarup Bhattacharjee, and T. Satyanarayana17.1 Introduction17.2 Production of glucoamylase: Microbes, substrate, nutrients, and fermentation system17.3 Thermophilic and mesophilic fungal glucoamylases17.4 Production of native glucoamylases17.5 Recombinant glucoamylases17.6 Multiple molecular forms of glucoamylases17.7 Structural characteristics of glucoamylases17.8 Biotechnological applications of glucoamylase17.9 Role of glucoamylase in starch conversion to sugar syrup17.10 Role of glucoamylase in HFCS17.11 Role of glucoamylase in the brewing and baking industry17.12 ConclusionReferencesIndex

“…one of the most recent additions to the Foundation and Frontiers in Enzymology series…. [that] aims to meet the knowledge requirements of scientists working in both academic and industry on the utilization of glycohydrolases for the production of pharmaceuticals, paper, and renewable fuels…. [A] concise, well-illustrated survey of the features of a variety of glycohydrolases…. [which] best serves as a point of entry for individuals wishing to learn more about this family of enzymes as a whole.” -- ©Doody’s Review Service, 2023, Peter J. Kennelly, PhD (Virginia Tech)